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GeneBe API Showcase

This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.

API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.

Documentation & Advanced Usage

Complete API documentation:docs.genebe.net/docs/api/overview/

Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/

Python client for pandas:pypi.org/project/genebe/

Java CLI for VCF files:github.com/pstawinski/genebe-cli

All tools documented at:docs.genebe.net

API Request Examples for Variant: 16-56519791-G-A (hg38)

Bash / cURL Example

bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=56519791&ref=G&alt=A&genome=hg38&allGenes=true"

API Response

json
{
  "variants": [
    {
      "chr": "16",
      "pos": 56519791,
      "ref": "G",
      "alt": "A",
      "effect": "synonymous_variant",
      "transcript": "NM_031885.5",
      "consequences": [
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "NM_031885.5",
          "protein_id": "NP_114091.4",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "ENST00000245157.11",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_031885.5"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": true,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000245157.11",
          "protein_id": "ENSP00000245157.5",
          "transcript_support_level": 1,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": "NM_031885.5",
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000245157.11"
        },
        {
          "aa_ref": null,
          "aa_alt": null,
          "canonical": false,
          "protein_coding": false,
          "strand": false,
          "consequences": [
            "intron_variant"
          ],
          "exon_rank": null,
          "exon_rank_end": null,
          "exon_count": 12,
          "intron_rank": 1,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "n.131+166C>T",
          "hgvs_p": null,
          "transcript": "ENST00000565781.6",
          "protein_id": null,
          "transcript_support_level": 1,
          "aa_start": null,
          "aa_end": null,
          "aa_length": null,
          "cds_start": null,
          "cds_end": null,
          "cds_length": null,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "retained_intron",
          "feature": "ENST00000565781.6"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000682188.1",
          "protein_id": "ENSP00000507655.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 736,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2211,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000682188.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "NM_001377456.1",
          "protein_id": "NP_001364385.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "NM_001377456.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000682047.1",
          "protein_id": "ENSP00000507699.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000682047.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000682205.1",
          "protein_id": "ENSP00000508377.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000682205.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000682470.1",
          "protein_id": "ENSP00000507654.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000682470.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000682855.1",
          "protein_id": "ENSP00000507027.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000682855.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 18,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000854960.1",
          "protein_id": "ENSP00000525019.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 721,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2166,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000854960.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000966325.1",
          "protein_id": "ENSP00000636384.1",
          "transcript_support_level": null,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 717,
          "cds_start": 72,
          "cds_end": null,
          "cds_length": 2154,
          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000966325.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
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          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000854962.1",
          "protein_id": "ENSP00000525021.1",
          "transcript_support_level": null,
          "aa_start": 24,
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          "aa_length": 710,
          "cds_start": 72,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "Y",
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          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
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          "exon_count": 17,
          "intron_rank": null,
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          "gene_symbol": "BBS2",
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          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000854961.1",
          "protein_id": "ENSP00000525020.1",
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          "cds_start": 72,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000854961.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000683858.1",
          "protein_id": "ENSP00000507657.1",
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          "cdna_start": null,
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        {
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          ],
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          "intron_rank": null,
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          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000923962.1",
          "protein_id": "ENSP00000594021.1",
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          "cds_start": 72,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
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          "biotype": "protein_coding",
          "feature": "ENST00000923962.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 1,
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          "exon_count": 17,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000923963.1",
          "protein_id": "ENSP00000594022.1",
          "transcript_support_level": null,
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          "aa_end": null,
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          "cds_start": 72,
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
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          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000684635.1",
          "protein_id": "ENSP00000507335.1",
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "Y",
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          "canonical": false,
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          "strand": false,
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          "intron_rank": null,
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          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
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          "transcript": "ENST00000966324.1",
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          "biotype": "protein_coding",
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        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
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          "strand": false,
          "consequences": [
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          ],
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          "intron_rank": null,
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          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000682482.1",
          "protein_id": "ENSP00000507903.1",
          "transcript_support_level": null,
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          "cdna_start": null,
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          "cdna_length": null,
          "mane_select": null,
          "mane_plus": null,
          "biotype": "protein_coding",
          "feature": "ENST00000682482.1"
        },
        {
          "aa_ref": "Y",
          "aa_alt": "Y",
          "canonical": false,
          "protein_coding": true,
          "strand": false,
          "consequences": [
            "synonymous_variant"
          ],
          "exon_rank": 1,
          "exon_rank_end": null,
          "exon_count": 16,
          "intron_rank": null,
          "intron_rank_end": null,
          "gene_symbol": "BBS2",
          "gene_hgnc_id": 967,
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr",
          "transcript": "ENST00000568104.6",
          "protein_id": "ENSP00000456289.1",
          "transcript_support_level": 5,
          "aa_start": 24,
          "aa_end": null,
          "aa_length": 675,
          "cds_start": 72,
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          "cdna_start": null,
          "cdna_end": null,
          "cdna_length": null,
          "mane_select": null,
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      "gene_symbol": "BBS2",
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      "dbsnp": "rs121908175",
      "frequency_reference_population": 6.8428005e-7,
      "hom_count_reference_population": 0,
      "allele_count_reference_population": 1,
      "gnomad_exomes_af": 6.8428e-7,
      "gnomad_genomes_af": null,
      "gnomad_exomes_ac": 1,
      "gnomad_genomes_ac": null,
      "gnomad_exomes_homalt": 0,
      "gnomad_genomes_homalt": null,
      "gnomad_mito_homoplasmic": null,
      "gnomad_mito_heteroplasmic": null,
      "computational_score_selected": -0.4099999964237213,
      "computational_prediction_selected": "Benign",
      "computational_source_selected": "BayesDel_noAF",
      "splice_score_selected": 0.009999999776482582,
      "splice_prediction_selected": "Benign",
      "splice_source_selected": "max_spliceai",
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      "alphamissense_score": null,
      "alphamissense_prediction": null,
      "bayesdelnoaf_score": -0.41,
      "bayesdelnoaf_prediction": "Benign",
      "phylop100way_score": 2.798,
      "phylop100way_prediction": "Benign",
      "spliceai_max_score": 0.01,
      "spliceai_max_prediction": "Benign",
      "dbscsnv_ada_score": null,
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      "apogee2_score": null,
      "apogee2_prediction": null,
      "mitotip_score": null,
      "mitotip_prediction": null,
      "acmg_score": -1,
      "acmg_classification": "Likely_benign",
      "acmg_criteria": "PM2,BP4_Moderate,BP7",
      "acmg_by_gene": [
        {
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          "benign_score": 3,
          "pathogenic_score": 2,
          "criteria": [
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            "BP4_Moderate",
            "BP7"
          ],
          "verdict": "Likely_benign",
          "transcript": "NM_031885.5",
          "gene_symbol": "BBS2",
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          "effects": [
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          "inheritance_mode": "AD,AR",
          "hgvs_c": "c.72C>T",
          "hgvs_p": "p.Tyr24Tyr"
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      ],
      "clinvar_disease": "Bardet-Biedl syndrome 2",
      "clinvar_classification": "Uncertain significance",
      "clinvar_review_status": "no assertion criteria provided",
      "clinvar_submissions_summary": "null",
      "phenotype_combined": "Bardet-Biedl syndrome 2",
      "pathogenicity_classification_combined": "Uncertain significance",
      "custom_annotations": null
    }
  ],
  "message": null
}